Grabbing
dataframe
type_markers <- FindAllMarkers(SO4, only.pos = TRUE)
## Calculating cluster type_1
## Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: `PackageCheck()` was deprecated in SeuratObject 5.0.0.
## ℹ Please use `rlang::check_installed()` instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
## (default method for FindMarkers) please install the presto package
## --------------------------------------------
## install.packages('devtools')
## devtools::install_github('immunogenomics/presto')
## --------------------------------------------
## After installation of presto, Seurat will automatically use the more
## efficient implementation (no further action necessary).
## This message will be shown once per session
## Calculating cluster type_2a
## Calculating cluster type_2b
## Calculating cluster type_2c
## Calculating cluster type_3
## Calculating cluster type_4
type_markers %>%
group_by(cluster) %>%
dplyr::filter(avg_log2FC > 1)
# Filter for your top genes and arrang, replace top_genes with genes I may want to analyze specifically.
df <- type_markers %>%
filter(gene %in% top_genes) %>%
arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers <- DEG_list %>% mutate(SYMBOL = gene)
ENTREZ_list <- bitr(
geneID = DEG_list$gene,
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)
## 'select()' returned 1:1 mapping between keys and columns
markers <- ENTREZ_list %>% inner_join(markers, by = "SYMBOL")
# Removing genes that are not statistically significant.
markers <- markers %>% dplyr::filter(p_val_adj < 0.05)
#head(markers, n = 50)
pos.markers <- markers %>% dplyr::filter(avg_log2FC > 0.5) %>% arrange(desc(abs(avg_log2FC)))
#head(pos.markers, n = 50)
pos.ranks <- pos.markers$ENTREZID[abs(pos.markers$avg_log2FC) > 0]
#head(pos.ranks)
pos_go <- enrichGO(gene = pos.ranks, #a vector of entrez gene id
OrgDb = "org.Mm.eg.db",
ont = "BP",
readable = TRUE) #whether mapping gene ID to gene Name
pos_go
## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:33] "11475" "16149" "14960" "27411" "14961" "12955" "13645" "16476" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...170 enriched terms found
## 'data.frame': 170 obs. of 12 variables:
## $ ID : chr "GO:0006883" "GO:0002478" "GO:0055075" "GO:0019884" ...
## $ Description : chr "intracellular sodium ion homeostasis" "antigen processing and presentation of exogenous peptide antigen" "potassium ion homeostasis" "antigen processing and presentation of exogenous antigen" ...
## $ GeneRatio : chr "4/32" "4/32" "4/32" "4/32" ...
## $ BgRatio : chr "28/28928" "34/28928" "35/28928" "41/28928" ...
## $ RichFactor : num 0.1429 0.1176 0.1143 0.0976 0.0889 ...
## $ FoldEnrichment: num 129.1 106.4 103.3 88.2 80.4 ...
## $ zScore : num 22.6 20.5 20.2 18.6 17.7 ...
## $ pvalue : num 2.48e-08 5.59e-08 6.30e-08 1.21e-07 1.78e-07 ...
## $ p.adjust : num 2.30e-05 2.30e-05 2.30e-05 3.32e-05 3.68e-05 ...
## $ qvalue : num 1.29e-05 1.29e-05 1.29e-05 1.86e-05 2.06e-05 ...
## $ geneID : chr "Umod/Atp1a1/Atp1b1/Fxyd2" "Cd74/H2-Aa/H2-Ab1/H2-K1" "Umod/Atp1a1/Atp1b1/Fxyd2" "Cd74/H2-Aa/H2-Ab1/H2-K1" ...
## $ Count : int 4 4 4 4 4 3 3 4 5 3 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722
dotplot(pos_go) +
ggtitle("") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)) +
scale_y_discrete(position = "right",
labels = function(x) str_wrap(x, width = 25)) # Wrap y-axis labels to 2 lines
## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
Viewing genes of
top 50
pathway_type <- strsplit(pos_go$geneID, "/")
names(pathway_type) <- pos_go$Description
pathway_type
## $`intracellular sodium ion homeostasis`
## [1] "Umod" "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`antigen processing and presentation of exogenous peptide antigen`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "H2-K1"
##
## $`potassium ion homeostasis`
## [1] "Umod" "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`antigen processing and presentation of exogenous antigen`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "H2-K1"
##
## $`sodium ion homeostasis`
## [1] "Umod" "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`establishment or maintenance of transmembrane electrochemical gradient`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`intracellular potassium ion homeostasis`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`chaperone-mediated protein folding`
## [1] "Cd74" "Umod" "Hspa1a" "Hspa1b"
##
## $`protein folding`
## [1] "Cd74" "Cryab" "Umod" "Hspa1a" "Hspa1b"
##
## $`antigen processing and presentation of exogenous peptide antigen via MHC class II`
## [1] "Cd74" "H2-Aa" "H2-Ab1"
##
## $`sodium ion export across plasma membrane`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`protein refolding`
## [1] "Cryab" "Hspa1a" "Hspa1b"
##
## $`antigen processing and presentation of peptide antigen`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "H2-K1"
##
## $`antigen processing and presentation of peptide antigen via MHC class II`
## [1] "Cd74" "H2-Aa" "H2-Ab1"
##
## $`antigen processing and presentation of peptide or polysaccharide antigen via MHC class II`
## [1] "Cd74" "H2-Aa" "H2-Ab1"
##
## $`cellular response to cadmium ion`
## [1] "Jun" "Mt1" "Mt2"
##
## $`chaperone cofactor-dependent protein refolding`
## [1] "Cd74" "Hspa1a" "Hspa1b"
##
## $`negative regulation of growth`
## [1] "Cryab" "Hspa1a" "Hspa1b" "Mt1" "Mt2"
##
## $`regulation of fibroblast proliferation`
## [1] "Cd74" "Egf" "Jun" "Fth1"
##
## $`'de novo' post-translational protein folding`
## [1] "Cd74" "Hspa1a" "Hspa1b"
##
## $`antigen processing and presentation`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "H2-K1"
##
## $`'de novo' protein folding`
## [1] "Cd74" "Hspa1a" "Hspa1b"
##
## $`potassium ion import across plasma membrane`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`fibroblast proliferation`
## [1] "Cd74" "Egf" "Jun" "Fth1"
##
## $`response to cadmium ion`
## [1] "Jun" "Mt1" "Mt2"
##
## $`urea transport`
## [1] "Slc14a2" "Umod"
##
## $`positive regulation of monocyte differentiation`
## [1] "Cd74" "Jun"
##
## $`positive regulation of sodium ion export across plasma membrane`
## [1] "Atp1b1" "Fxyd2"
##
## $`regulation of microtubule nucleation`
## [1] "Hspa1a" "Hspa1b"
##
## $`regulation of sodium ion export across plasma membrane`
## [1] "Atp1b1" "Fxyd2"
##
## $`MHC class II protein complex assembly`
## [1] "H2-Aa" "H2-Ab1"
##
## $`peptide antigen assembly with MHC class II protein complex`
## [1] "H2-Aa" "H2-Ab1"
##
## $`positive regulation of cell activation`
## [1] "Acta2" "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`potassium ion transmembrane transport`
## [1] "Cd63" "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`stress response to metal ion`
## [1] "Mt1" "Mt2"
##
## $`positive regulation of fibroblast proliferation`
## [1] "Cd74" "Egf" "Jun"
##
## $`export across plasma membrane`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`protein stabilization`
## [1] "Cd74" "Cryab" "Hspa1b" "Atp1b1"
##
## $`positive regulation of leukocyte differentiation`
## [1] "Cd74" "H2-Aa" "Jun" "Actb"
##
## $`positive regulation of hemopoiesis`
## [1] "Cd74" "H2-Aa" "Jun" "Actb"
##
## $`leukocyte cell-cell adhesion`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Umod" "Actb"
##
## $`positive regulation of ERK1 and ERK2 cascade`
## [1] "Acta2" "Cd74" "Egf" "Jun"
##
## $`regulation of blood pressure`
## [1] "Acta2" "Umod" "Klk1" "Atp1a1"
##
## $`regulation of metal ion transport`
## [1] "Egf" "Cd63" "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`regulation of sodium ion transport`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`regulation of hemopoiesis`
## [1] "Cd74" "H2-Aa" "Jun" "Hspa1b" "Actb"
##
## $`MHC protein complex assembly`
## [1] "H2-Aa" "H2-Ab1"
##
## $`peptide antigen assembly with MHC protein complex`
## [1] "H2-Aa" "H2-Ab1"
##
## $`detoxification of inorganic compound`
## [1] "Mt1" "Mt2"
##
## $`negative regulation of peptidase activity`
## [1] "Cryab" "Hspa1b" "Wfdc2" "Cst3"
##
## $`regulation of protein-containing complex assembly`
## [1] "Cryab" "Hspa1a" "Hspa1b" "Tmsb4x" "H3f3b"
##
## $`potassium ion transport`
## [1] "Cd63" "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`response to heat`
## [1] "Cryab" "Hspa1a" "Hspa1b"
##
## $`cellular response to copper ion`
## [1] "Mt1" "Mt2"
##
## $`positive regulation of ubiquitin-dependent protein catabolic process`
## [1] "Egf" "Hspa1a" "Hspa1b"
##
## $`positive regulation of T cell activation`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`sodium ion transport`
## [1] "Umod" "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`regulation of monocyte differentiation`
## [1] "Cd74" "Jun"
##
## $`mitochondrial electron transport, cytochrome c to oxygen`
## [1] "Cox4i1" "Cox8a"
##
## $`cellular response to zinc ion`
## [1] "Mt1" "Mt2"
##
## $`positive regulation of leukocyte cell-cell adhesion`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`regulation of mitotic spindle assembly`
## [1] "Hspa1a" "Hspa1b"
##
## $`positive regulation of myeloid cell differentiation`
## [1] "Cd74" "Jun" "Hspa1b"
##
## $`tissue migration`
## [1] "Acta2" "Jun" "Cd63"
##
## $`negative regulation of hydrolase activity`
## [1] "Cryab" "Hspa1b" "Wfdc2" "Cst3"
##
## $`inorganic cation import across plasma membrane`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`inorganic ion import across plasma membrane`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`positive regulation of DNA metabolic process`
## [1] "Egf" "Jun" "Actb" "Cst3"
##
## $`positive regulation of sodium ion transmembrane transport`
## [1] "Atp1b1" "Fxyd2"
##
## $`positive regulation of T cell differentiation`
## [1] "Cd74" "H2-Aa" "Actb"
##
## $`positive regulation of proteolysis involved in protein catabolic process`
## [1] "Egf" "Hspa1a" "Hspa1b"
##
## $`one-carbon compound transport`
## [1] "Slc14a2" "Umod"
##
## $`nitric oxide mediated signal transduction`
## [1] "Mt1" "Mt2"
##
## $`regulation of ERK1 and ERK2 cascade`
## [1] "Acta2" "Cd74" "Egf" "Jun"
##
## $`positive regulation of cell-cell adhesion`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`microtubule polymerization or depolymerization`
## [1] "Cryab" "Hspa1a" "Hspa1b"
##
## $`intracellular zinc ion homeostasis`
## [1] "Mt1" "Mt2"
##
## $`positive regulation of lymphocyte activation`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`positive regulation of lymphocyte differentiation`
## [1] "Cd74" "H2-Aa" "Actb"
##
## $`negative regulation of proteolysis`
## [1] "Cryab" "Hspa1b" "Wfdc2" "Cst3"
##
## $`positive regulation of microtubule polymerization`
## [1] "Hspa1a" "Hspa1b"
##
## $`response to copper ion`
## [1] "Mt1" "Mt2"
##
## $`regulation of spindle assembly`
## [1] "Hspa1a" "Hspa1b"
##
## $`oxidative phosphorylation`
## [1] "Cox6c" "Cox4i1" "Cox8a"
##
## $`ERK1 and ERK2 cascade`
## [1] "Acta2" "Cd74" "Egf" "Jun"
##
## $`regulation of protein stability`
## [1] "Cd74" "Cryab" "Hspa1b" "Atp1b1"
##
## $`positive regulation of receptor internalization`
## [1] "Egf" "Cd63"
##
## $`regulation of leukocyte differentiation`
## [1] "Cd74" "H2-Aa" "Jun" "Actb"
##
## $`proton transmembrane transport`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`positive regulation of leukocyte activation`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`microtubule nucleation`
## [1] "Hspa1a" "Hspa1b"
##
## $`positive regulation of microtubule polymerization or depolymerization`
## [1] "Hspa1a" "Hspa1b"
##
## $`regulation of ubiquitin-dependent protein catabolic process`
## [1] "Egf" "Hspa1a" "Hspa1b"
##
## $`regulation of leukocyte cell-cell adhesion`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`regulation of T cell activation`
## [1] "Cd74" "H2-Aa" "H2-Ab1" "Actb"
##
## $`regulation of peptidase activity`
## [1] "Cryab" "Hspa1b" "Wfdc2" "Cst3"
##
## $`response to temperature stimulus`
## [1] "Cryab" "Hspa1a" "Hspa1b"
##
## $`regulation of sodium ion transmembrane transporter activity`
## [1] "Atp1b1" "Fxyd2"
##
## $`regulation of supramolecular fiber organization`
## [1] "Cryab" "Hspa1a" "Hspa1b" "Tmsb4x"
##
## $`monocyte differentiation`
## [1] "Cd74" "Jun"
##
## $`regulation of mitotic spindle organization`
## [1] "Hspa1a" "Hspa1b"
##
## $`defense response to bacterium`
## [1] "Umod" "Wfdc15b" "Wfdc2" "H2-K1"
##
## $`sodium ion transmembrane transport`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`positive regulation of sodium ion transport`
## [1] "Atp1b1" "Fxyd2"
##
## $`regulation of spindle organization`
## [1] "Hspa1a" "Hspa1b"
##
## $`negative regulation of cell growth`
## [1] "Cryab" "Hspa1a" "Hspa1b"
##
## $`response to zinc ion`
## [1] "Mt1" "Mt2"
##
## $`positive regulation of DNA replication`
## [1] "Jun" "Cst3"
##
## $`regulation of actin filament-based movement`
## [1] "Acta2" "Atp1a1"
##
## $`regulation of T cell differentiation`
## [1] "Cd74" "H2-Aa" "Actb"
##
## $`membrane repolarization`
## [1] "Atp1a1" "Atp1b1"
##
## $`cellular response to metal ion`
## [1] "Jun" "Mt1" "Mt2"
##
## $`aerobic respiration`
## [1] "Cox6c" "Cox4i1" "Cox8a"
##
## $`regulation of transmembrane transporter activity`
## [1] "Actb" "Atp1b1" "Fxyd2"
##
## $`regulation of protein polymerization`
## [1] "Hspa1a" "Hspa1b" "Tmsb4x"
##
## $`import across plasma membrane`
## [1] "Atp1a1" "Atp1b1" "Fxyd2"
##
## $`regulation of transporter activity`
## [1] "Actb" "Atp1b1" "Fxyd2"
##
## $`regulation of microtubule polymerization`
## [1] "Hspa1a" "Hspa1b"
##
## $`regulation of sodium ion transmembrane transport`
## [1] "Atp1b1" "Fxyd2"
##
## $`sister chromatid segregation`
## [1] "Hspa1a" "Hspa1b" "Actb"
##
## $`positive regulation of cytokine-mediated signaling pathway`
## [1] "Cd74" "Hspa1b"
##
## $`positive regulation of interleukin-8 production`
## [1] "Cd74" "Hspa1b"
##
## $`regulation of lymphocyte differentiation`
## [1] "Cd74" "H2-Aa" "Actb"
##
## $`regulation of proteolysis involved in protein catabolic process`
## [1] "Egf" "Hspa1a" "Hspa1b"
##
## $`regulation of myeloid cell differentiation`
## [1] "Cd74" "Jun" "Hspa1b"
##
## $`positive regulation of receptor-mediated endocytosis`
## [1] "Egf" "Cd63"
##
## $`aerobic electron transport chain`
## [1] "Cox4i1" "Cox8a"
##
## $`negative regulation of cysteine-type endopeptidase activity involved in apoptotic process`
## [1] "Cryab" "Hspa1b"
##
## $`positive regulation of response to cytokine stimulus`
## [1] "Cd74" "Hspa1b"
##
## $`regulation of cardiac muscle contraction`
## [1] "Atp1a1" "Atp1b1"
##
## $`mitotic spindle assembly`
## [1] "Hspa1a" "Hspa1b"
##
## $`cellular respiration`
## [1] "Cox6c" "Cox4i1" "Cox8a"
##
## $`positive regulation of myeloid leukocyte differentiation`
## [1] "Cd74" "Jun"
##
## $`regulation of interleukin-8 production`
## [1] "Cd74" "Hspa1b"
##
## $`regulation of epithelial cell migration`
## [1] "Jun" "Cd63"
##
## $`positive regulation of proteasomal ubiquitin-dependent protein catabolic process`
## [1] "Hspa1a" "Hspa1b"
##
## $`interleukin-8 production`
## [1] "Cd74" "Hspa1b"
##
## $`ameboidal-type cell migration`
## [1] "Acta2" "Jun" "Cd63"
##
## $`mitochondrial ATP synthesis coupled electron transport`
## [1] "Cox4i1" "Cox8a"
##
## $`negative regulation of cysteine-type endopeptidase activity`
## [1] "Cryab" "Hspa1b"
##
## $`mitotic nuclear division`
## [1] "Egf" "Hspa1a" "Hspa1b"
##
## $`ATP synthesis coupled electron transport`
## [1] "Cox4i1" "Cox8a"
##
## $`regulation of potassium ion transmembrane transport`
## [1] "Cd63" "Atp1b1"
##
## $`protein polymerization`
## [1] "Hspa1a" "Hspa1b" "Tmsb4x"
##
## $`regulation of striated muscle contraction`
## [1] "Atp1a1" "Atp1b1"
##
## $`regulation of receptor internalization`
## [1] "Egf" "Cd63"
##
## $`peptidyl-threonine phosphorylation`
## [1] "Egf" "Umod"
##
## $`microtubule polymerization`
## [1] "Hspa1a" "Hspa1b"
##
## $`positive regulation of protein polymerization`
## [1] "Hspa1a" "Hspa1b"
##
## $`regulation of microtubule polymerization or depolymerization`
## [1] "Hspa1a" "Hspa1b"
##
## $`tumor necrosis factor-mediated signaling pathway`
## [1] "Umod" "Hspa1b"
##
## $`nuclear chromosome segregation`
## [1] "Hspa1a" "Hspa1b" "Actb"
##
## $`muscle contraction`
## [1] "Acta2" "Atp1a1" "Atp1b1"
##
## $`actin-mediated cell contraction`
## [1] "Acta2" "Atp1a1"
##
## $`positive regulation of endothelial cell proliferation`
## [1] "Egf" "Jun"
##
## $`peptidyl-threonine modification`
## [1] "Egf" "Umod"
##
## $`positive regulation of proteolysis`
## [1] "Egf" "Hspa1a" "Hspa1b"
##
## $`regulation of monoatomic cation transmembrane transport`
## [1] "Cd63" "Atp1b1" "Fxyd2"
##
## $`regulation of potassium ion transport`
## [1] "Cd63" "Atp1b1"
##
## $`cellular response to chemical stress`
## [1] "Jun" "Atp1a1" "Cst3"
##
## $`epithelial cell migration`
## [1] "Jun" "Cd63"
##
## $`T cell differentiation`
## [1] "Cd74" "H2-Aa" "Actb"
##
## $`regulation of binding`
## [1] "Egf" "Jun" "Actb"
##
## $`positive regulation of proteasomal protein catabolic process`
## [1] "Hspa1a" "Hspa1b"
##
## $`regulation of DNA binding`
## [1] "Egf" "Jun"
##
## $`epithelium migration`
## [1] "Jun" "Cd63"
##
## $`regulation of endocytosis`
## [1] "Egf" "Actb" "Cd63"
##
## $`antibacterial humoral response`
## [1] "Wfdc15b" "Wfdc2"
##
## $`respiratory electron transport chain`
## [1] "Cox4i1" "Cox8a"
##
## $`response to unfolded protein`
## [1] "Umod" "Hspa1a"
gyarmati <- c("Fabp3", "Egf", "Ccn1", "Foxq1", "Cxcl12", "Vash2", "Pamr1", "Vegfa", "Ccn3", "Bmp3", "Fgf9", "Spp1", "Wnt10a", "Sfrp1", "Tcf4", "Pappa2", "Unc5d", "Sema3c", "Robo2", "Slit2", "Egfl6", "Hgfac", "Pdgfc", "Megf9", "Frem1", "Thsd4", "Spock2", "Mmp14", "Adamtsl2", "Car8", "Irx1", "Irx2", "Hoxd11", "Hoxc4", "Etv1")
# Filter for your top genes and arrang, replace top_genes with genes I may want to analyze specifically.
df <- type_markers %>%
filter(gene %in% gyarmati) %>%
arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers <- DEG_list %>% mutate(SYMBOL = gene)
ENTREZ_list <- bitr(
geneID = DEG_list$gene,
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)
## 'select()' returned 1:1 mapping between keys and columns
markers <- ENTREZ_list %>% inner_join(markers, by = "SYMBOL")
# Removing genes that are not statistically significant.
markers <- markers %>% dplyr::filter(p_val_adj < 0.05)
#head(markers, n = 50)
pos.markers <- markers %>% dplyr::filter(avg_log2FC > 0.5) %>% arrange(desc(abs(avg_log2FC)))
#head(pos.markers, n = 50)
pos.ranks <- pos.markers$ENTREZID[abs(pos.markers$avg_log2FC) > 0]
#head(pos.ranks)
pos_go <- enrichGO(gene = pos.ranks, #a vector of entrez gene id
OrgDb = "org.Mm.eg.db",
ont = "BP",
readable = TRUE) #whether mapping gene ID to gene Name
pos_go
## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:25] "15220" "13645" "14077" "16007" "20315" "94214" "23850" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...282 enriched terms found
## 'data.frame': 282 obs. of 12 variables:
## $ ID : chr "GO:0060562" "GO:0007411" "GO:0097485" "GO:0048705" ...
## $ Description : chr "epithelial tube morphogenesis" "axon guidance" "neuron projection guidance" "skeletal system morphogenesis" ...
## $ GeneRatio : chr "7/24" "6/24" "6/24" "6/24" ...
## $ BgRatio : chr "404/28928" "258/28928" "259/28928" "269/28928" ...
## $ RichFactor : num 0.0173 0.0233 0.0232 0.0223 0.0289 ...
## $ FoldEnrichment: num 20.9 28 27.9 26.9 34.8 ...
## $ zScore : num 11.6 12.6 12.5 12.3 12.9 ...
## $ pvalue : num 2.77e-08 5.59e-08 5.72e-08 7.15e-08 2.80e-07 ...
## $ p.adjust : num 1.67e-05 1.67e-05 1.67e-05 1.67e-05 4.88e-05 ...
## $ qvalue : num 7.64e-06 7.64e-06 7.64e-06 7.64e-06 2.23e-05 ...
## $ geneID : chr "Egf/Cxcl12/Mmp14/Irx1/Hoxd11/Irx2/Vegfa" "Cxcl12/Unc5d/Etv1/Robo2/Megf9/Vegfa" "Cxcl12/Unc5d/Etv1/Robo2/Megf9/Vegfa" "Pappa2/Frem1/Mmp14/Hoxc4/Hoxd11/Vegfa" ...
## $ Count : int 7 6 6 6 5 5 5 6 4 4 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722
dotplot(pos_go) +
ggtitle("") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)) +
scale_y_discrete(position = "right",
labels = function(x) str_wrap(x, width = 25)) # Wrap y-axis labels to 2 lines
## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
Viewing gyarmati
genes vvia pathway
pathway_type <- strsplit(pos_go$geneID, "/")
names(pathway_type) <- pos_go$Description
pathway_type
## $`epithelial tube morphogenesis`
## [1] "Egf" "Cxcl12" "Mmp14" "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`axon guidance`
## [1] "Cxcl12" "Unc5d" "Etv1" "Robo2" "Megf9" "Vegfa"
##
## $`neuron projection guidance`
## [1] "Cxcl12" "Unc5d" "Etv1" "Robo2" "Megf9" "Vegfa"
##
## $`skeletal system morphogenesis`
## [1] "Pappa2" "Frem1" "Mmp14" "Hoxc4" "Hoxd11" "Vegfa"
##
## $`kidney epithelium development`
## [1] "Robo2" "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`endothelial cell proliferation`
## [1] "Egf" "Cxcl12" "Vash2" "Mmp14" "Vegfa"
##
## $`branching morphogenesis of an epithelial tube`
## [1] "Egf" "Cxcl12" "Mmp14" "Hoxd11" "Vegfa"
##
## $`cell-substrate adhesion`
## [1] "Ccn1" "Spock2" "Frem1" "Egfl6" "Mmp14" "Vegfa"
##
## $`nephron tubule morphogenesis`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`nephron epithelium morphogenesis`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`nephron morphogenesis`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`renal tubule morphogenesis`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`morphogenesis of a branching epithelium`
## [1] "Egf" "Cxcl12" "Mmp14" "Hoxd11" "Vegfa"
##
## $`cartilage development`
## [1] "Ccn1" "Ccn3" "Bmp3" "Hoxc4" "Hoxd11"
##
## $`regulation of cell-substrate adhesion`
## [1] "Ccn1" "Spock2" "Egfl6" "Mmp14" "Vegfa"
##
## $`metanephros development`
## [1] "Robo2" "Irx1" "Hoxd11" "Irx2"
##
## $`positive regulation of endothelial cell proliferation`
## [1] "Egf" "Cxcl12" "Vash2" "Vegfa"
##
## $`morphogenesis of a branching structure`
## [1] "Egf" "Cxcl12" "Mmp14" "Hoxd11" "Vegfa"
##
## $`kidney morphogenesis`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`nephron tubule development`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`bone morphogenesis`
## [1] "Pappa2" "Frem1" "Mmp14" "Hoxd11"
##
## $`renal tubule development`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`proximal/distal pattern formation`
## [1] "Irx1" "Hoxd11" "Irx2"
##
## $`nephron epithelium development`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`positive regulation of cell-substrate adhesion`
## [1] "Ccn1" "Spock2" "Egfl6" "Vegfa"
##
## $`connective tissue development`
## [1] "Ccn1" "Ccn3" "Bmp3" "Hoxc4" "Hoxd11"
##
## $`regulation of endothelial cell proliferation`
## [1] "Egf" "Cxcl12" "Vash2" "Vegfa"
##
## $`epithelial tube formation`
## [1] "Egf" "Irx1" "Irx2" "Vegfa"
##
## $`kidney development`
## [1] "Robo2" "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`nephron development`
## [1] "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $`tube formation`
## [1] "Egf" "Irx1" "Irx2" "Vegfa"
##
## $`renal system development`
## [1] "Robo2" "Irx1" "Hoxd11" "Irx2" "Vegfa"
##
## $regionalization
## [1] "Robo2" "Irx1" "Hoxc4" "Hoxd11" "Irx2"
##
## $`regulation of protein localization to early endosome`
## [1] "Egf" "Vegfa"
##
## $`positive regulation of protein localization to early endosome`
## [1] "Egf" "Vegfa"
##
## $`regulation of chemotaxis`
## [1] "Cxcl12" "Ccn3" "Robo2" "Vegfa"
##
## $chemotaxis
## [1] "Ccn1" "Cxcl12" "Ccn3" "Robo2" "Vegfa"
##
## $`endothelial cell migration`
## [1] "Egf" "Cxcl12" "Ccn3" "Vegfa"
##
## $taxis
## [1] "Ccn1" "Cxcl12" "Ccn3" "Robo2" "Vegfa"
##
## $`loop of Henle development`
## [1] "Irx1" "Irx2"
##
## $`positive regulation of epithelial cell proliferation`
## [1] "Egf" "Cxcl12" "Vash2" "Vegfa"
##
## $`bone development`
## [1] "Pappa2" "Frem1" "Mmp14" "Hoxd11"
##
## $`myeloid leukocyte migration`
## [1] "Cxcl12" "Ccn3" "Mmp14" "Vegfa"
##
## $`regulation of leukocyte migration`
## [1] "Cxcl12" "Ccn3" "Mmp14" "Vegfa"
##
## $`positive regulation of protein localization to endosome`
## [1] "Egf" "Vegfa"
##
## $`regulation of Notch signaling pathway`
## [1] "Ccn3" "Robo2" "Mmp14"
##
## $`induction of positive chemotaxis`
## [1] "Cxcl12" "Vegfa"
##
## $`regulation of protein localization to endosome`
## [1] "Egf" "Vegfa"
##
## $`positive regulation of axonogenesis`
## [1] "Cxcl12" "Robo2" "Vegfa"
##
## $`regulation of animal organ morphogenesis`
## [1] "Robo2" "Hoxd11" "Vegfa"
##
## $`regulation of axon extension involved in axon guidance`
## [1] "Cxcl12" "Vegfa"
##
## $`protein localization to early endosome`
## [1] "Egf" "Vegfa"
##
## $`craniofacial suture morphogenesis`
## [1] "Frem1" "Mmp14"
##
## $`embryonic skeletal system morphogenesis`
## [1] "Mmp14" "Hoxc4" "Hoxd11"
##
## $`ureteric bud development`
## [1] "Robo2" "Hoxd11" "Vegfa"
##
## $`mesonephric epithelium development`
## [1] "Robo2" "Hoxd11" "Vegfa"
##
## $`mesonephric tubule development`
## [1] "Robo2" "Hoxd11" "Vegfa"
##
## $`mesonephros development`
## [1] "Robo2" "Hoxd11" "Vegfa"
##
## $`segment specification`
## [1] "Irx1" "Irx2"
##
## $`regulation of vasculature development`
## [1] "Cxcl12" "Vash2" "Tcf4" "Vegfa"
##
## $`axon extension involved in axon guidance`
## [1] "Cxcl12" "Vegfa"
##
## $`mammary gland alveolus development`
## [1] "Egf" "Vegfa"
##
## $`mammary gland lobule development`
## [1] "Egf" "Vegfa"
##
## $`neuron projection extension involved in neuron projection guidance`
## [1] "Cxcl12" "Vegfa"
##
## $`extracellular matrix organization`
## [1] "Ccn1" "Spock2" "Egfl6" "Mmp14"
##
## $`regulation of ERK1 and ERK2 cascade`
## [1] "Egf" "Ccn1" "Cxcl12" "Vegfa"
##
## $`external encapsulating structure organization`
## [1] "Ccn1" "Spock2" "Egfl6" "Mmp14"
##
## $`extracellular structure organization`
## [1] "Ccn1" "Spock2" "Egfl6" "Mmp14"
##
## $`retinal ganglion cell axon guidance`
## [1] "Robo2" "Vegfa"
##
## $`nephron tubule formation`
## [1] "Irx1" "Irx2"
##
## $`regulation of vascular endothelial growth factor signaling pathway`
## [1] "Tcf4" "Vegfa"
##
## $`ERK1 and ERK2 cascade`
## [1] "Egf" "Ccn1" "Cxcl12" "Vegfa"
##
## $`organ induction`
## [1] "Robo2" "Hoxd11"
##
## $`regulation of cellular response to vascular endothelial growth factor stimulus`
## [1] "Tcf4" "Vegfa"
##
## $`striated muscle cell differentiation`
## [1] "Cxcl12" "Ccn3" "Mmp14" "Vegfa"
##
## $`regulation of leukocyte chemotaxis`
## [1] "Cxcl12" "Ccn3" "Vegfa"
##
## $`positive regulation of positive chemotaxis`
## [1] "Cxcl12" "Vegfa"
##
## $`labyrinthine layer blood vessel development`
## [1] "Ccn1" "Vash2"
##
## $`myotube differentiation`
## [1] "Cxcl12" "Ccn3" "Mmp14"
##
## $`chondrocyte proliferation`
## [1] "Ccn3" "Mmp14"
##
## $`regulation of positive chemotaxis`
## [1] "Cxcl12" "Vegfa"
##
## $`embryonic skeletal system development`
## [1] "Mmp14" "Hoxc4" "Hoxd11"
##
## $`regulation of mononuclear cell migration`
## [1] "Cxcl12" "Ccn3" "Mmp14"
##
## $`endothelial cell chemotaxis`
## [1] "Ccn3" "Vegfa"
##
## $`regulation of animal organ formation`
## [1] "Robo2" "Hoxd11"
##
## $`leukocyte migration`
## [1] "Cxcl12" "Ccn3" "Mmp14" "Vegfa"
##
## $`protein localization to endosome`
## [1] "Egf" "Vegfa"
##
## $`positive regulation of receptor internalization`
## [1] "Egf" "Vegfa"
##
## $`positive regulation of cartilage development`
## [1] "Ccn1" "Hoxd11"
##
## $`regulation of monocyte chemotaxis`
## [1] "Cxcl12" "Ccn3"
##
## $`regulation of epithelial cell proliferation`
## [1] "Egf" "Cxcl12" "Vash2" "Vegfa"
##
## $`regulation of axonogenesis`
## [1] "Cxcl12" "Robo2" "Vegfa"
##
## $`positive regulation of leukocyte migration`
## [1] "Cxcl12" "Mmp14" "Vegfa"
##
## $`positive regulation of vasculature development`
## [1] "Cxcl12" "Vash2" "Vegfa"
##
## $`regulation of cell growth`
## [1] "Cxcl12" "Ccn3" "Mmp14" "Vegfa"
##
## $`placenta blood vessel development`
## [1] "Ccn1" "Vash2"
##
## $`specification of animal organ identity`
## [1] "Robo2" "Hoxd11"
##
## $`developmental induction`
## [1] "Robo2" "Hoxd11"
##
## $`positive regulation of animal organ morphogenesis`
## [1] "Robo2" "Hoxd11"
##
## $`Notch signaling pathway`
## [1] "Ccn3" "Robo2" "Mmp14"
##
## $`vascular endothelial growth factor signaling pathway`
## [1] "Tcf4" "Vegfa"
##
## $`metanephric nephron development`
## [1] "Irx1" "Irx2"
##
## $`positive regulation of morphogenesis of an epithelium`
## [1] "Egf" "Vegfa"
##
## $`branching involved in blood vessel morphogenesis`
## [1] "Cxcl12" "Vegfa"
##
## $`regulation of myotube differentiation`
## [1] "Ccn3" "Mmp14"
##
## $`positive regulation of Notch signaling pathway`
## [1] "Ccn3" "Robo2"
##
## $`negative regulation of chemotaxis`
## [1] "Ccn3" "Robo2"
##
## $`muscle cell differentiation`
## [1] "Cxcl12" "Ccn3" "Mmp14" "Vegfa"
##
## $`positive regulation of cell growth`
## [1] "Cxcl12" "Mmp14" "Vegfa"
##
## $`positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction`
## [1] "Egf" "Cxcl12" "Vegfa"
##
## $`dopaminergic neuron differentiation`
## [1] "Cxcl12" "Vegfa"
##
## $`monocyte chemotaxis`
## [1] "Cxcl12" "Ccn3"
##
## $`neuron migration`
## [1] "Cxcl12" "Unc5d" "Vegfa"
##
## $`positive regulation of ERK1 and ERK2 cascade`
## [1] "Egf" "Cxcl12" "Vegfa"
##
## $`mononuclear cell migration`
## [1] "Cxcl12" "Ccn3" "Mmp14"
##
## $`negative regulation of leukocyte migration`
## [1] "Cxcl12" "Ccn3"
##
## $`positive regulation of axon extension`
## [1] "Cxcl12" "Vegfa"
##
## $`regulation of calcium ion import`
## [1] "Egf" "Cxcl12"
##
## $`cell-matrix adhesion`
## [1] "Frem1" "Mmp14" "Vegfa"
##
## $`heart valve morphogenesis`
## [1] "Ccn1" "Robo2"
##
## $`osteoblast differentiation`
## [1] "Ccn1" "Bmp3" "Vegfa"
##
## $`leukocyte chemotaxis`
## [1] "Cxcl12" "Ccn3" "Vegfa"
##
## $`positive chemotaxis`
## [1] "Cxcl12" "Vegfa"
##
## $`cellular response to vascular endothelial growth factor stimulus`
## [1] "Tcf4" "Vegfa"
##
## $`labyrinthine layer development`
## [1] "Ccn1" "Vash2"
##
## $`regulation of focal adhesion assembly`
## [1] "Mmp14" "Vegfa"
##
## $`regulation of cell-substrate junction assembly`
## [1] "Mmp14" "Vegfa"
##
## $`positive regulation of receptor-mediated endocytosis`
## [1] "Egf" "Vegfa"
##
## $`response to mechanical stimulus`
## [1] "Cxcl12" "Etv1" "Mmp14"
##
## $`positive regulation of ossification`
## [1] "Ccn1" "Ccn3"
##
## $`branching involved in ureteric bud morphogenesis`
## [1] "Hoxd11" "Vegfa"
##
## $`heart valve development`
## [1] "Ccn1" "Robo2"
##
## $`regulation of cell-substrate junction organization`
## [1] "Mmp14" "Vegfa"
##
## $`ameboidal-type cell migration`
## [1] "Cxcl12" "Ccn3" "Vegfa"
##
## $`syncytium formation by plasma membrane fusion`
## [1] "Cxcl12" "Vash2"
##
## $`cell-cell fusion`
## [1] "Cxcl12" "Vash2"
##
## $`endochondral bone morphogenesis`
## [1] "Mmp14" "Hoxd11"
##
## $`syncytium formation`
## [1] "Cxcl12" "Vash2"
##
## $`positive regulation of DNA biosynthetic process`
## [1] "Egf" "Vegfa"
##
## $`regulation of morphogenesis of an epithelium`
## [1] "Egf" "Vegfa"
##
## $`animal organ formation`
## [1] "Robo2" "Hoxd11"
##
## $`ureteric bud morphogenesis`
## [1] "Hoxd11" "Vegfa"
##
## $`regulation of cartilage development`
## [1] "Ccn1" "Hoxd11"
##
## $`regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction`
## [1] "Egf" "Cxcl12" "Vegfa"
##
## $`heart morphogenesis`
## [1] "Ccn1" "Robo2" "Vegfa"
##
## $`positive regulation of osteoblast differentiation`
## [1] "Ccn1" "Vegfa"
##
## $`ovarian follicle development`
## [1] "Mmp14" "Vegfa"
##
## $`mesonephric tubule morphogenesis`
## [1] "Hoxd11" "Vegfa"
##
## $`positive regulation of neural precursor cell proliferation`
## [1] "Egf" "Vegfa"
##
## $`cardiac septum morphogenesis`
## [1] "Ccn1" "Robo2"
##
## $`regulation of angiogenesis`
## [1] "Vash2" "Tcf4" "Vegfa"
##
## $`cranial skeletal system development`
## [1] "Frem1" "Mmp14"
##
## $`outflow tract morphogenesis`
## [1] "Robo2" "Vegfa"
##
## $`focal adhesion assembly`
## [1] "Mmp14" "Vegfa"
##
## $`positive regulation of growth`
## [1] "Cxcl12" "Mmp14" "Vegfa"
##
## $`negative regulation of cell adhesion`
## [1] "Cxcl12" "Mmp14" "Vegfa"
##
## $`calcium ion import`
## [1] "Egf" "Cxcl12"
##
## $`ventricular septum development`
## [1] "Ccn1" "Robo2"
##
## $`positive regulation of neurogenesis`
## [1] "Cxcl12" "Robo2" "Vegfa"
##
## $`regulation of cellular response to growth factor stimulus`
## [1] "Ccn1" "Tcf4" "Vegfa"
##
## $`cell chemotaxis`
## [1] "Cxcl12" "Ccn3" "Vegfa"
##
## $`positive regulation of proteolysis`
## [1] "Egf" "Ccn1" "Mmp14"
##
## $`phosphatidylinositol 3-kinase/protein kinase B signal transduction`
## [1] "Egf" "Cxcl12" "Vegfa"
##
## $`regulation of receptor internalization`
## [1] "Egf" "Vegfa"
##
## $`embryonic organ morphogenesis`
## [1] "Mmp14" "Hoxc4" "Hoxd11"
##
## $`cell-substrate junction assembly`
## [1] "Mmp14" "Vegfa"
##
## $`negative regulation of locomotion`
## [1] "Cxcl12" "Ccn3" "Robo2"
##
## $`regulation of axon extension`
## [1] "Cxcl12" "Vegfa"
##
## $`sensory perception of pain`
## [1] "Cxcl12" "Ccn3"
##
## $`cell-substrate junction organization`
## [1] "Mmp14" "Vegfa"
##
## $`positive regulation of mononuclear cell migration`
## [1] "Cxcl12" "Mmp14"
##
## $`regulation of striated muscle cell differentiation`
## [1] "Ccn3" "Mmp14"
##
## $`regulation of DNA biosynthetic process`
## [1] "Egf" "Vegfa"
##
## $`positive regulation of endothelial cell migration`
## [1] "Egf" "Vegfa"
##
## $`positive regulation of leukocyte chemotaxis`
## [1] "Cxcl12" "Vegfa"
##
## $`positive regulation of nervous system development`
## [1] "Cxcl12" "Robo2" "Vegfa"
##
## $`positive regulation of neuron differentiation`
## [1] "Cxcl12" "Tcf4"
##
## $segmentation
## [1] "Irx1" "Irx2"
##
## $`embryonic placenta development`
## [1] "Ccn1" "Vash2"
##
## $`regulation of extent of cell growth`
## [1] "Cxcl12" "Vegfa"
##
## $`positive regulation of lipid biosynthetic process`
## [1] "Fabp3" "Ccn1"
##
## $`chondrocyte differentiation`
## [1] "Ccn3" "Hoxd11"
##
## $`artery development`
## [1] "Robo2" "Vegfa"
##
## $`blood vessel endothelial cell migration`
## [1] "Cxcl12" "Vegfa"
##
## $`cardiac septum development`
## [1] "Ccn1" "Robo2"
##
## $`regulation of cell-matrix adhesion`
## [1] "Mmp14" "Vegfa"
##
## $`axon extension`
## [1] "Cxcl12" "Vegfa"
##
## $`female gonad development`
## [1] "Mmp14" "Vegfa"
##
## $`regulation of neural precursor cell proliferation`
## [1] "Egf" "Vegfa"
##
## $`development of primary female sexual characteristics`
## [1] "Mmp14" "Vegfa"
##
## $`regulation of receptor-mediated endocytosis`
## [1] "Egf" "Vegfa"
##
## $`regulation of ossification`
## [1] "Ccn1" "Ccn3"
##
## $`positive regulation of cell projection organization`
## [1] "Cxcl12" "Robo2" "Vegfa"
##
## $`embryonic epithelial tube formation`
## [1] "Irx1" "Irx2"
##
## $`cardiac chamber morphogenesis`
## [1] "Ccn1" "Robo2"
##
## $`regulation of neurogenesis`
## [1] "Cxcl12" "Robo2" "Vegfa"
##
## $`cardiac ventricle development`
## [1] "Ccn1" "Robo2"
##
## $`regulation of lipid transport`
## [1] "Egf" "Fabp3"
##
## $`regulation of osteoblast differentiation`
## [1] "Ccn1" "Vegfa"
##
## $`receptor internalization`
## [1] "Egf" "Vegfa"
##
## $`regulation of cerebellar granule cell precursor proliferation`
## [1] "Egf"
##
## $`positive regulation of dopamine secretion`
## [1] "Cxcl12"
##
## $`chorio-allantoic fusion`
## [1] "Ccn1"
##
## $`coronary artery morphogenesis`
## [1] "Vegfa"
##
## $`regulation of phosphatidylcholine metabolic process`
## [1] "Fabp3"
##
## $`positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis`
## [1] "Vegfa"
##
## $`regulation of blood-brain barrier permeability`
## [1] "Vegfa"
##
## $`regulation of muscle cell differentiation`
## [1] "Ccn3" "Mmp14"
##
## $`female sex differentiation`
## [1] "Mmp14" "Vegfa"
##
## $`positive regulation of chemotaxis`
## [1] "Cxcl12" "Vegfa"
##
## $`positive regulation of peptidyl-tyrosine phosphorylation`
## [1] "Egf" "Vegfa"
##
## $`germ cell migration`
## [1] "Cxcl12"
##
## $`regulation of nitric oxide mediated signal transduction`
## [1] "Vegfa"
##
## $`post-embryonic camera-type eye development`
## [1] "Vegfa"
##
## $`astrocyte cell migration`
## [1] "Mmp14"
##
## $`negative regulation of endothelial cell differentiation`
## [1] "Vegfa"
##
## $`positive regulation of lipid metabolic process`
## [1] "Fabp3" "Ccn1"
##
## $`DNA biosynthetic process`
## [1] "Egf" "Vegfa"
##
## $`regulation of cysteine-type endopeptidase activity involved in apoptotic process`
## [1] "Ccn1" "Vegfa"
##
## $`mammary gland development`
## [1] "Egf" "Vegfa"
##
## $`regulation of endothelial cell migration`
## [1] "Egf" "Vegfa"
##
## $`endothelial cell activation`
## [1] "Tcf4"
##
## $`primitive hemopoiesis`
## [1] "Vegfa"
##
## $`lung vasculature development`
## [1] "Vegfa"
##
## $`positive regulation of phospholipid biosynthetic process`
## [1] "Fabp3"
##
## $`positive regulation of angiogenesis`
## [1] "Vash2" "Vegfa"
##
## $`morphogenesis of embryonic epithelium`
## [1] "Irx1" "Irx2"
##
## $`negative regulation of cellular extravasation`
## [1] "Cxcl12"
##
## $`negative regulation of sterol transport`
## [1] "Egf"
##
## $`negative regulation of cholesterol transport`
## [1] "Egf"
##
## $`venous blood vessel morphogenesis`
## [1] "Vegfa"
##
## $`embryonic skeletal joint morphogenesis`
## [1] "Hoxd11"
##
## $`regulation of lipid localization`
## [1] "Egf" "Fabp3"
##
## $`mast cell chemotaxis`
## [1] "Vegfa"
##
## $`bone trabecula formation`
## [1] "Vegfa"
##
## $`regulation of protein kinase C signaling`
## [1] "Vegfa"
##
## $`regulation of ceramide biosynthetic process`
## [1] "Ccn1"
##
## $`placenta development`
## [1] "Ccn1" "Vash2"
##
## $`neuron projection extension`
## [1] "Cxcl12" "Vegfa"
##
## $`positive regulation of endocytosis`
## [1] "Egf" "Vegfa"
##
## $`cardiac chamber development`
## [1] "Ccn1" "Robo2"
##
## $`positive regulation of myotube differentiation`
## [1] "Mmp14"
##
## $`hyaluronan biosynthetic process`
## [1] "Egf"
##
## $`positive regulation of osteoblast proliferation`
## [1] "Ccn1"
##
## $`glial cell-derived neurotrophic factor receptor signaling pathway`
## [1] "Mmp14"
##
## $`commissural neuron axon guidance`
## [1] "Vegfa"
##
## $`vascular associated smooth muscle cell development`
## [1] "Vegfa"
##
## $`motor neuron migration`
## [1] "Vegfa"
##
## $`positive regulation of chemokine (C-X-C motif) ligand 2 production`
## [1] "Ccn1"
##
## $`regulation of cysteine-type endopeptidase activity`
## [1] "Ccn1" "Vegfa"
##
## $`smooth muscle cell proliferation`
## [1] "Ccn3" "Vegfa"
##
## $`cell proliferation in external granule layer`
## [1] "Egf"
##
## $`cerebellar granule cell precursor proliferation`
## [1] "Egf"
##
## $`negative regulation of focal adhesion assembly`
## [1] "Mmp14"
##
## $`embryonic skeletal joint development`
## [1] "Hoxd11"
##
## $`regulation of sphingolipid biosynthetic process`
## [1] "Ccn1"
##
## $`negative regulation of cell-substrate junction organization`
## [1] "Mmp14"
##
## $`negative regulation of dendritic cell apoptotic process`
## [1] "Cxcl12"
##
## $`positive regulation of endothelial cell chemotaxis`
## [1] "Vegfa"
##
## $`regulation of cell size`
## [1] "Cxcl12" "Vegfa"
##
## $`heart field specification`
## [1] "Robo2"
##
## $`mechanosensory behavior`
## [1] "Etv1"
##
## $`negative regulation of myotube differentiation`
## [1] "Ccn3"
##
## $`cell proliferation in hindbrain`
## [1] "Egf"
##
## $`phospholipid homeostasis`
## [1] "Fabp3"
##
## $`atrial septum morphogenesis`
## [1] "Ccn1"
##
## $`cardiac vascular smooth muscle cell differentiation`
## [1] "Vegfa"
##
## $`epithelial cell-cell adhesion`
## [1] "Ccn3"
##
## $`mast cell migration`
## [1] "Vegfa"
##
## $`regulation of trophoblast cell migration`
## [1] "Vegfa"
##
## $`regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis`
## [1] "Vegfa"
##
## $`positive regulation of phospholipid metabolic process`
## [1] "Fabp3"
##
## $`regulation of cell-cell adhesion mediated by cadherin`
## [1] "Vegfa"
##
## $`negative regulation of cell-cell adhesion`
## [1] "Cxcl12" "Vegfa"
##
## $`positive regulation of developmental growth`
## [1] "Cxcl12" "Vegfa"
##
## $`negative regulation of secretion`
## [1] "Egf" "Ccn3"
##
## $`negative regulation of neuron apoptotic process`
## [1] "Foxq1" "Vegfa"
##
## $`tissue remodeling`
## [1] "Mmp14" "Vegfa"
##
## $`positive regulation of catecholamine secretion`
## [1] "Cxcl12"
##
## $`negative regulation of bone resorption`
## [1] "Vegfa"
##
## $`bone trabecula morphogenesis`
## [1] "Vegfa"
##
## $`trophoblast cell migration`
## [1] "Vegfa"
# Research -> top genes that appear in all cluster
VlnPlot(SO4, features = c("Bmp3", "Fgf9", "Spp1", "Wnt10a", "Sfrp1", "Tcf4"))
## Warning: The `slot` argument of `FetchData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# accurate
# Research -> top enriched genes that show clustering according to Gyarmati
VlnPlot(SO4, features = c("Fabp3", "Egf", "Ccn1", "Foxq1", "Cxcl12", "Vash2", "Pamr1", "Vegfa", "Nov"),group.by = "subclass2_MD", ncol = 3)
## Warning: The following requested variables were not found: Nov
VlnPlot(SO4, features = c("Fabp3", "Egf", "Ccn1", "Foxq1", "Cxcl12", "Vash2", "Pamr1", "Vegfa", "Nov"), ncol = 3)
## Warning: The following requested variables were not found: Nov
gene_group <- list(
Angiogenesis = c("Unc5d", "Vash2", "Cxcl14", "Sfrp1", "Pamr1", "Pappa2"),
Migration_Patterning = c("Sema3c", "Robo2", "Slit2", "Bmp3", "Egfl6", "Fgf9"),
Growth_Factors = c("Vegfd", "Hgfac", "Pdgfc", "Megf9", "Frem1", "Thsd4"),
ECM_Remodeling = c("Spock2", "Mmp14", "Adamtsl2", "Car8"),
Transcription_GrowthFactors = c("Irx1", "Irx2", "Wnt10a", "Hoxd11", "Hoxc4", "Etv1")
)
Angiogenesis_genes <- gene_group$Angiogenesis
Migration_Patterning_genes <- gene_group$Migration_Patterning
Growth_Factors_genes <- gene_group$Growth_Factors
ECM_Remodeling_genes <- gene_group$ECM_Remodeling
Transcription_GrowthFactors_genes <- gene_group$Transcription_GrowthFactors
VlnPlot(SO4,features = Angiogenesis_genes)
VlnPlot(SO4,features = Migration_Patterning_genes)
VlnPlot(SO4,features = Growth_Factors_genes)
VlnPlot(SO4,features = ECM_Remodeling_genes)
VlnPlot(SO4,features = Transcription_GrowthFactors_genes)
